Classes | |
| class | AddHydrogenProcessor |
| Saturate atoms with hydrogen atoms. More... | |
| class | AtomTyper |
| Base class for a programable Atom typer. More... | |
| class | BuildBondsProcessor |
| Bond creation processor. More... | |
| class | ClearChargeProcessor |
| Clears the charge on all atoms. More... | |
| class | ClearRadiusProcessor |
| Clears the radius of all atoms. More... | |
| class | AssignRadiusProcessor |
| Assigns the radius to each atom. More... | |
| class | AssignChargeProcessor |
| Assigns a charge to each atom. More... | |
| class | FragmentDB |
| FragmentDB - fragment database class. More... | |
| class | TransformationProcessor |
| Transformation applicator. More... | |
| class | HBondProcessor |
| This processor computes all hydrogen bonds occuring between amino acids in the composite it is applied to. More... | |
| class | Kekuliser |
| Class to transform bonds with type "aromatic" to conjugated single and double bonds. More... | |
| class | NodeItem< Node, Edge > |
| The node type in a molecular graph. More... | |
| class | ReconstructFragmentProcessor |
| ReconstructFragmentProcessor. More... | |
| class | ResidueChecker |
| Residue Consistency Checker. More... | |
| class | SecondaryStructureProcessor |
| Secondary structure extraction from 3D structure. More... | |
| class | UCK |
| Unique Chemical Key. More... | |
Type definitions | |
| typedef std::list< String > | Peptides::ThreeLetterAASequence |
| An amino acid sequence in three-letter code. | |
| typedef String | Peptides::OneLetterAASequence |
| An amino acid sequence in one-letter code. | |
Amino acid sequence conversion | |
| BALL_EXPORT char | Peptides::OneLetterCode (const String &aa) |
| Convert a three-letter amino acid name to the one-letter abbreviation. | |
| BALL_EXPORT String | Peptides::ThreeLetterCode (char aa) |
| Convert a one-letter amino acid abbreviation to its three-letter code. | |
| BALL_EXPORT OneLetterAASequence | Peptides::ThreeLetterToOneLetter (const ThreeLetterAASequence &sequence) |
| Convert an amino acid sequence from three-letter code to one-letter code. | |
| BALL_EXPORT ThreeLetterAASequence | Peptides::OneLetterToThreeLetter (const OneLetterAASequence &sequence) |
| Convert an amino acid sequence from one-letter code to three-letter code. | |
| BALL_EXPORT OneLetterAASequence | Peptides::GetSequence (const Protein &protein) |
| Get amino acid sequence from an protein. | |
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Get amino acid sequence from an protein. This method iterates over all residues of the protein, calls OneLetterCode for each of the residue names, and returns the concatenation of all results. |
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Convert a three-letter amino acid name to the one-letter abbreviation.
If the string given is not the three-letter code of one of the twenty amino acids, |
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Convert an amino acid sequence from one-letter code to three-letter code. Call ThreeLetterCode for each of the characters in the string. |
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Convert a one-letter amino acid abbreviation to its three-letter code.
If the character given is not the code for one of the twenty amino acids, |
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Convert an amino acid sequence from three-letter code to one-letter code. Call OneLetterCode for each of the amino acids in the sequence. |